Evaluate gene sets by cell type-specific gene expression
Wei Sun
2024-07-10
Setup
Check the expression of each gene set in each brain-related cell type
Read in gene info and gene set assignments
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
length(assayed_genes)## [1] 2000gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 41 43 44 44 45 46## [1] 40## [1] 41 41 42 42 43 43 43 43 43 43 43 43 43 43 44 44 44 44 44 44 44 45 45 45 45
## [26] 45 45 45 45 45 45 45 45 45 45 45 45 45 45 46Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"##
## FALSE TRUE
## 1643 357##
## FALSE TRUE <NA>
## 21 1622 357gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: BTBD11 ABTB3
## 2: LINC01006 RNF32-DT
## 3: LINC01185 REL-DT
## 4: ZRANB2-AS2 ZRANB2-DT
## 5: LINC00271 AHI1-DT
## 6: RFX3-AS1 RFX3-DT
## 7: COX10-AS1 COX10-DT
## 8: SUCLG2-AS1 SUCLG2-DT
## 9: C5orf17 LINC02899
## 10: OSMR-AS1 OSMR-DT
## 11: C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2 TENM2-AS1
## 13: LINC00637 PPP1R13B-DT
## 14: MPP6 MPHOSPH6
## 15: C7orf61 SPACDR
## 16: C3orf35 APRG1
## 17: HRAT92 PDGFA-DT
## 18: LINC00884 ATP13A3-DT
## 19: LINC01137 ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21: MAFG-DT MILIP
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## 3: ASB4 ASB4 ASB4
## 4: USH1C USH1C USH1C
## 5: ARHGAP44 ARHGAP44 ARHGAP44## t1
## 1
## 2000Read in cell type-specific expression data
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
## [1] 1587110 4## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5## [1] 79##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090## [1] 16 2## Cell_type Cell_group
## 1: Excitatory neurons Neuronal
## 2: Inhibitory neurons Neuronal##
## Astrocytes B-cells
## 20090 20090
## Bipolar cells Cone photoreceptor cells
## 20090 20090
## Excitatory neurons Horizontal cells
## 20090 20090
## Inhibitory neurons Microglial cells
## 20090 20090
## Muller glia cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Plasma cells
## 20090 20090
## Rod photoreceptor cells Schwann cells
## 20090 20090
## T-cells
## 20090Check gene expression for each gene set
## [1] 2000 3for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Cell type`) %in%
str_to_lower(cell_group$Cell_type)))
mat1 = match(str_to_lower(df$`Cell type`),
str_to_lower(cell_group$Cell_type))
df = cbind(df, cell_group[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
df$Cell_group = factor(df$Cell_group,
levels = unique(cell_group$Cell_group))
p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "ARHGAP44" "AMPH" "PLS3" "GABRE" "SH3D19" "WIPF1"
## [7] "RGS4" "UNC13A" "RFC3" "EPHB2" "BTBD11" "ABTB2"
## [13] "PCBP3" "STAC3" "ERC2" "IL1RAPL2" "ITGA3" "SYN1"
## [19] "TCOF1" "TRHDE" "RIMS1" "CDKL1" "CELF4" "PPFIBP1"
## [25] "KHDRBS2" "FGF12" "RIMS3" "KIAA1217" "BIN1" "SRRM4"
## [31] "ZNF385B" "ANK3" "SPTBN4" "EDIL3" "ZMAT4" "GRM5"
## [37] "REPS2" "NABP1" "RIMS2" "KCNQ5" "VSTM2B" "PTPRT"
## [43] "PARVA"
## [1] "found 42 genes."
## [1] 2
## [1] "SEMA3A" "TMEM241" "ALCAM" "THSD4"
## [5] "HLA-E" "DIO2" "RNF212B" "RP1-292B18.4"
## [9] "RP1-15D23.2" "RP4-660H19.1" "CCDC192" "LINC00326"
## [13] "GRM3-AS1" "LINC02250" "RBMS3-AS3" "RP11-475C16.2"
## [17] "RP11-657O9.1" "RP11-115N4.1" "MEF2C-AS2" "ZFPM2-AS1"
## [21] "LINC00923" "RP11-116O11.1" "LRRC24" "RP11-260G13.1"
## [25] "RP11-370I10.2" "DIO2-AS1" "TSIX" "SEMA3C"
## [29] "MAN1A1" "UST" "PAM" "ARID5B"
## [33] "ZNF385D" "MGAT5" "SEMA3D" "PLCL2"
## [37] "ART3" "ELAPOR2" "PPM1E" "SAMD12"
## [41] "RP11-191L9.4" "TSBP1-AS1" "RP1-35C21.2" "LINC01414"
## [1] "found 22 genes."
## [1] 3
## [1] "DNAH9" "MAOB" "TACR1" "LEPR" "COL4A2"
## [6] "LYPD6B" "IGFBP7" "METTL2B" "AGBL2" "DPP10"
## [11] "CP" "ATP9A" "SPAG1" "AGFG2" "ABCC3"
## [16] "ST8SIA1" "SERPINI2" "PRRX1" "KLHL29" "MOB3B"
## [21] "PLXDC2" "COL21A1" "HIVEP3" "PLCE1" "ENSA"
## [26] "KCNN3" "GRIK4" "ABR" "DHRS3" "LRRC2"
## [31] "ZNF704" "WNK2" "GNG4" "IFFO2" "NPAS2"
## [36] "PHYHD1" "APOLD1" "TSHZ2" "ZBTB7C" "RILPL1"
## [41] "TRPV1" "ZNF594-DT" "RP11-93B21.2"
## [1] "found 41 genes."
## [1] 4
## [1] "GDAP1L1" "MT1G" "AGBL3" "HHIP"
## [5] "CLMP" "MT1E" "MFSD4B" "SGCZ"
## [9] "FSIP2" "ANKUB1" "RP11-131L23.1" "TMLHE-AS1"
## [13] "ST7-AS2" "SNAP25-AS1" "Z83001.1" "PCDH9-AS2"
## [17] "AC009501.4" "GNG12-AS1" "LINC00513" "LINC01877"
## [21] "RP5-1101C3.1" "PTPRG-AS1" "ZBTB20-AS5" "RORA-AS1"
## [25] "C1QTNF7-AS1" "RP11-223C24.1" "LINC01618" "RP11-517I3.1"
## [29] "CTD-3239E11.2" "RP11-649G15.2" "MPPED2-AS1" "BBOX1-AS1"
## [33] "CTD-2537O9.1" "RP11-315E17.1" "LINC01579" "RP11-184D12.1"
## [37] "LINC01572" "PRKCA-AS1" "LINC02664" "CH17-140K24.2"
## [41] "RP11-470M1.2" "RP11-589M4.5" "RP11-221G19.1" "RP11-555K12.4"
## [45] "DISP3"
## [1] "found 11 genes."
## [1] 5
## [1] "HHAT" "PEX5L" "DNAH6" "PEBP4"
## [5] "EFCAB11" "MLIP" "SPATA17" "STPG2"
## [9] "ODAD2" "DNAH12" "RFLNA" "WDR97"
## [13] "ENO4" "PIWIL2" "HMGN5" "CRPPA"
## [17] "LGALSL-DT" "CHL1-AS2" "LINC01876" "AC105760.2"
## [21] "LINC01185" "AC008269.2" "PATL2" "RPL34-DT"
## [25] "LINC01524" "DRAIC" "CTB-161M19.4" "LINC01182"
## [29] "CTC-347C20.1" "CTB-178M22.2" "RP11-727A23.10" "RP11-511B23.2"
## [33] "RP11-352M15.1" "SPESP1" "RP11-525K10.3" "RP11-396B14.2"
## [37] "RP11-397A16.1" "LINC00506" "RP5-847G17.1" "RP11-444C24.1"
## [41] "RP11-96C13.1" "RP11-520F22.1" "DNAH5" "AC104088.1"
## [1] "found 18 genes."
## [1] 6
## [1] "PON3" "TENT5A" "MTERF1" "PKIB"
## [5] "SCN11A" "CATSPERE" "LINC01006" "GPR39"
## [9] "COL25A1" "CC2D2B" "RP11-306O13.1" "COL28A1"
## [13] "AC026188.1" "POT1-AS1" "PLCG1-AS1" "AC012593.1"
## [17] "SOX21-AS1" "LYPLAL1-DT" "LNC-LBCS" "HDAC2-AS2"
## [21] "LINC01277" "LINC01937" "LINC01239" "PPP1R9A-AS1"
## [25] "AC079305.11" "RP11-4B14.3" "NECTIN3-AS1" "RP11-167H9.4"
## [29] "RP11-436F23.1" "LINC02196" "RP11-404I7.2" "LINC00534"
## [33] "RP11-804N13.1" "RMST" "PRANCR" "RP11-72M17.1"
## [37] "AC004158.3" "CTC-498M16.4" "RP11-69G16.2" "RP4-660H19.2"
## [41] "RP3-383B8.1" "RP11-346I3.7" "RP1-84D21.2" "RP11-120J1.2"
## [45] "RP11-168F16.1"
## [1] "found 10 genes."
## [1] 7
## [1] "MRC2" "ABCC2" "IDI1" "RIPK2" "EPM2A" "HES1"
## [7] "PPP1R3C" "BCL2L14" "EEPD1" "MT2A" "ID1" "IFI6"
## [13] "APOE" "CCDC59" "GULP1" "CCDC102B" "SETBP1" "GRIA4"
## [19] "LMOD1" "SYNPR" "HNF4G" "PAPPA" "CALN1" "KCTD16"
## [25] "CCSER1" "PDXP" "ARHGAP8" "MRPL33" "TLE2" "KNOP1"
## [31] "FSD1" "USP9Y" "PDE1A" "ARID3A" "DOCK10" "MCPH1"
## [37] "NLGN4Y" "CKB" "NXNL1" "TTTY14" "UTY" "MITF"
## [43] "LINC00278"
## [1] "found 41 genes."
## [1] 8
## [1] "BID" "GAB2" "SDK2" "BLVRB" "SLC39A14" "GMDS"
## [7] "SIPA1L2" "PRR5L" "CADPS" "HPRT1" "SNTB1" "GLRX"
## [13] "HEG1" "ROBO2" "MALAT1" "CD99" "GAS7" "VRK2"
## [19] "DOK5" "COTL1" "BNIP3L" "SIPA1L3" "ZMIZ1" "GAB1"
## [25] "TANC1" "ECE1" "TSHZ3" "ZFP36" "RFTN1" "TNS3"
## [31] "GABPB2" "DIAPH2" "ZEB1" "DGKZ" "ADCY9" "EVA1C"
## [37] "IRS1" "BCL2" "ANO6" "SYN3" "IRS2" "PLCG2"
## [43] "CPEB1"
## [1] "found 42 genes."
## [1] 9
## [1] "SLC26A8" "WDR64" "LINC01931" "GLIPR1L1"
## [5] "P2RY14" "HEPN1" "AC002463.3" "RP11-547I7.1"
## [9] "AC017101.10" "RP11-141A19.1" "RP11-417B4.2" "GNA14-AS1"
## [13] "RP11-46O21.2" "GPC5-AS2" "AC037445.1" "PCDH9-AS4"
## [17] "RP11-666F17.1" "RP11-109I13.2" "STARD13-AS" "GS1-433O24.1"
## [21] "AC008067.2" "RP13-143G15.4" "LINC00960" "RP11-768G7.3"
## [25] "GK-AS1" "LRP4-AS1" "ANK2-AS1" "MAPK10-AS1"
## [29] "RP11-120A1.1" "RP11-39E3.3" "STPG2-AS1" "RP11-351A11.1"
## [33] "RP11-463D19.1" "AP000462.2" "RP11-513G19.1" "A2ML1-AS1"
## [37] "RP11-39M21.1" "CRIM1-DT" "RP11-58G13.1" "AC005786.7"
## [41] "RP11-138H11.1" "CTD-2282P23.2" "RP11-576O3.1" "RP11-394G3.3"
## [45] "RP11-66G15.1"
## [1] "found 5 genes."
## [1] 10
## [1] "APBA1" "DHRS7B" "FAXC" "ABHD3" "ARHGAP31" "APBA2"
## [7] "RRP12" "DGKG" "CDON" "PFKP" "PHACTR3" "MYO9B"
## [13] "PALM" "CAB39L" "EEF2K" "SYT17" "OLFM2" "COBL"
## [19] "LIN7A" "CCND3" "TFDP2" "FOXO3" "HIF3A" "HIP1"
## [25] "RIN2" "MAPK4" "NFIC" "BOC" "ARHGAP26" "TIAM2"
## [31] "FAM171A1" "FOXO1" "C2CD2" "AHCYL2" "EPB41" "FBXO27"
## [37] "ZFPM2" "FAM222B" "PACS1" "CADM1" "ANKS1B" "DMWD"
## [43] "DACH1"
## [1] "found 43 genes."
## [1] 11
## [1] "PNPLA3" "GALNT16" "ELAVL2" "SLC2A9" "PPM1H" "ACAT2"
## [7] "PTH1R" "PBX3" "TMEM51" "CERS6" "CES2" "SMYD3"
## [13] "PCLO" "PDE4A" "RASAL2" "PIR" "CERS4" "MAST3"
## [19] "PLIN3" "UBE2R2" "SH3PXD2A" "LRRC4B" "SLC39A11" "NAV1"
## [25] "SSH2" "ITPKB" "SNTG1" "CACNA1B" "FSIP1" "MAGI1"
## [31] "AKAP6" "CLSTN2" "PKNOX2" "PLEKHA7" "LDLRAD4" "PTPN9"
## [37] "CMTM4" "RALYL" "ELAVL3" "RYR2" "PCAT1"
## [1] "found 40 genes."
## [1] 12
## [1] "PCSK1N" "SRPX2" "POLR2I" "LRRC9"
## [5] "H3-3B" "CA1" "ITGA9" "LRTM1"
## [9] "CHST9" "SHOC1" "FILIP1L" "DLEU1"
## [13] "TSBP1" "MT1H" "AC105461.1" "ASTN2-AS1"
## [17] "RP4-613B23.1" "DPP10-AS3" "IPO9-AS1" "DPP10-AS1"
## [21] "LINC02877" "PRKAR2B-AS1" "RP11-274H2.2" "BAALC-AS1"
## [25] "CTD-2015H6.3" "RP11-711G10.1" "RP11-452H21.1" "AP000487.6"
## [29] "RP11-1H15.2" "RP11-867G2.8" "RP11-144F15.1" "RP11-887P2.5"
## [33] "RP11-363J20.2" "HIF1A-AS3" "CTC-513N18.6" "RP11-355F16.1"
## [37] "RP11-80I3.1" "SLC7A14-AS1" "RP11-793H13.14" "CTD-2172F7.1"
## [41] "RP11-725F23.1" "RP11-875G18.1" "NUP210L" "SMOC1"
## [45] "TTTY10"
## [1] "found 15 genes."
## [1] 13
## [1] "CD38" "CALCRL" "SIDT1" "CCDC80"
## [5] "IFI44L" "SLC24A4" "SAXO1" "PKD1L1"
## [9] "CD200R1" "ADAMTS9" "GUCY1A1" "KIF6"
## [13] "FREM1" "VWA3B" "NRG4" "DELEC1"
## [17] "VWA3A" "SCOC-AS1" "STUM" "RP11-735G4.1"
## [21] "LINC01515" "RP11-106M7.1" "DIRC3" "DIRC3-AS1"
## [25] "LINC01695" "AC007563.5" "RP11-132E11.2" "RP11-624M8.1"
## [29] "RP11-114J13.1" "NEUROG2-AS1" "VCAN-AS1" "RP11-669M16.1"
## [33] "LINC02715" "RP11-708B6.2" "MAP1LC3B2" "FRMD6-AS2"
## [37] "PTCSC3" "RP11-323P17.2" "RP11-290O12.2" "CTC-490G23.6"
## [41] "RP11-274G22.1" "RP11-364P22.4" "RP11-373E16.6" "CTD-2040G12.2"
## [45] "RP11-423B13.1"
## [1] "found 18 genes."
## [1] 14
## [1] "XK" "CTD-2313D3.2" "FAP" "SLCO1A2"
## [5] "LAMB4" "CATSPERG" "CACNA1I" "DNAH11"
## [9] "TGIF2" "AK7" "CCDC3" "GAL3ST2"
## [13] "TDRD9" "DRC1" "CFAP251" "SHROOM4"
## [17] "ZNF653" "ARMC3" "PPP1R36" "PDZRN4"
## [21] "C2" "TVP23A" "TEKT1" "ATOH8"
## [25] "GSG1L" "NOTUM" "C7orf61" "CFAP54"
## [29] "ODAD4" "LINC01208" "NRSN2-AS1" "AC092155.4"
## [33] "ARL17B" "HMGA1P4" "RP5-827C21.2" "KCNK15-AS1"
## [37] "CTB-35F21.1" "RP11-279O9.4" "LINC02315" "LINC02356"
## [41] "RP11-876N24.2" "CTD-2189E23.1" "SPANXA2-OT1" "RP11-301F14.1"
## [45] "CTD-2201E18.6"
## [1] "found 27 genes."
## [1] 15
## [1] "CDH10" "PRKCQ" "MBNL3" "EPHA6" "TRPM3" "MT3" "CEMIP"
## [8] "SCG3" "SLC1A2" "EPHA4" "AKAP12" "EMP1" "CD72" "ABCA12"
## [15] "TMEM108" "CXCL14" "ACSL1" "WIF1" "GALNT10" "DLC1" "LRRC3B"
## [22] "EXT1" "CMSS1" "KLHL32" "GCNT1" "BRINP2" "ATP1A2" "MCF2L2"
## [29] "NGEF" "PLXNA2" "SESN1" "KIF3C" "STAG1" "VAV3" "CPM"
## [36] "CEP350" "SHROOM3" "CRADD" "PCDH7" "SWI5" "NCKAP5" "LSMEM2"
## [43] "EFNA5" "S100A10"
## [1] "found 44 genes."
## [1] 16
## [1] "MAP3K7CL" "LRRIQ3" "MN1" "RHCE"
## [5] "AC074391.1" "PPP1R26-AS1" "EPS15-AS1" "XIST"
## [9] "LINC02884" "LINC01934" "LINC00886" "SUCLG2-AS1"
## [13] "LINC01301" "LINC00637" "RP11-692P14.1" "GRK3"
## [17] "RIPOR2" "TFCP2L1" "DMGDH" "GMPR"
## [21] "MRAS" "VWA5B1" "RFTN2" "FAXDC2"
## [25] "CHST11" "LDLRAD3" "NWD1" "TMEM184B"
## [29] "PLIN5" "LINC00598" "PDYN-AS1" "ARHGEF26-AS1"
## [33] "RTL9" "ALDH1L1-AS2" "STX18-AS1" "RP11-150C16.1"
## [37] "RP11-838N2.5" "AC079610.1" "RP11-711K1.8" "RP11-358F13.1"
## [41] "RP1-166D18.1" "RP11-26L21.1" "RP11-166M16.1" "RP11-421A16.1"
## [45] "RP11-404C6.6"
## [1] "found 19 genes."
## [1] 17
## [1] "AHRR" "CPED1" "WNT5B" "DNAH7"
## [5] "APOC1" "CABLES1" "C10orf90" "AXDND1"
## [9] "HOPX" "TMEM132C" "CCBE1" "RFX8"
## [13] "NPSR1-AS1" "LINC01117" "LINC01768" "CENATAC-DT"
## [17] "RP11-496B10.6" "SAMD4A" "PPP1R15A" "ISYNA1"
## [21] "CPEB3" "TPD52L1" "C1orf21" "WLS"
## [25] "PDZRN3" "TOX2" "SLC22A23" "GLTP"
## [29] "ADAMTS10" "SDK1" "DOC2A" "PID1"
## [33] "GNA14" "ZNF208" "CACNB2" "GPR176"
## [37] "DHRSX" "GNG7" "CTD-2527I21.15" "AJAP1"
## [41] "TOX" "LINC00511" "HPN-AS1"
## [1] "found 35 genes."
## [1] 18
## [1] "USH1C" "ATP11A"
## [3] "MGAT3" "NXN"
## [5] "GTF2IRD1" "HDAC9"
## [7] "PDZD4" "ITPKC"
## [9] "RELB" "AEBP1"
## [11] "CDH23" "WASF1"
## [13] "IL1R1" "PADI2"
## [15] "ZC4H2" "QRICH2"
## [17] "GALNT8" "ZSWIM4"
## [19] "PTPRE" "TMTC1"
## [21] "IRAK2" "DENND2A"
## [23] "DOCK11" "RHPN1"
## [25] "ORAI2" "TMCO4"
## [27] "SHISA5" "TMC1"
## [29] "KIF5C" "HAP1"
## [31] "SPATA13_ENSG00000182957" "RTN4RL1"
## [33] "COL27A1" "RASGEF1A"
## [35] "NHSL2" "TCEA3"
## [37] "S1PR3" "MEF2B"
## [39] "LINC00685" "EPCAM-DT"
## [41] "L3MBTL2-AS1" "KLF2-DT"
## [43] "AF038458.3" "FBXO17"
## [45] "DGCR5_ENSG00000273032"
## [1] "found 38 genes."
## [1] 19
## [1] "SEL1L2" "RERG" "MAEL" "SLC22A3"
## [5] "ADRA1B" "PAH" "SLC24A3" "NAP1L3"
## [9] "CYP4X1" "DCHS2" "GRM3" "MRPS9-AS2"
## [13] "AP000282.2" "LINC01344" "AC007682.1" "AC009264.1"
## [17] "RP11-142A5.1" "RP11-154H17.1" "LINC02234" "HS3ST5"
## [21] "F11-AS1" "RP1-84O15.2" "RP11-317N12.1" "ZFHX4-AS1"
## [25] "RP11-541P9.3" "RP11-431M3.1" "RP11-134O21.1" "LINC02763"
## [29] "LINC02327" "RP11-526N18.1" "RP11-242P2.1" "PLS3-AS1"
## [33] "RP11-561I11.4" "LINC00540" "RP11-378A12.1" "LINC01727"
## [37] "CH17-174L20.1" "RP11-624A4.2" "CALCB" "FZD9"
## [41] "AC016745.3" "MEIKIN" "RP11-328J6.1" "RP11-237N2.1"
## [45] "RP11-183J19.1"
## [1] "found 15 genes."
## [1] 20
## [1] "ZFR2" "MOGAT1" "PUDP" "DPH6"
## [5] "TMEM132B" "SLC14A1" "KIAA1328" "DNAAF1"
## [9] "ERICH3" "HDHD5-AS1" "CLDN4" "FIRRE"
## [13] "LIPE-AS1" "FBXO16" "AC004540.5" "RP11-162D16.2"
## [17] "RP11-498J9.2" "AC079807.4" "MMADHC-DT" "RAP2C-AS1"
## [21] "RP11-120D5.1" "COX10-AS1" "RP11-410D17.2" "RP11-461O7.1"
## [25] "RP11-373N22.3" "LINC02144" "RP11-130F10.1" "RP11-284M14.1"
## [29] "RP11-679C8.2" "MAILR" "GS1-57L11.1" "RP11-156K13.1"
## [33] "RP11-20E24.1" "RP11-571L19.7" "RP11-524F11.2" "CTD-2349P21.11"
## [37] "ADGRL1-AS1" "GEMIN7-AS1" "RP11-413N10.3" "RP11-281A20.2"
## [41] "RP11-314E10.1" "RP11-563M4.2" "TPCN1" "C3orf35"
## [45] "AP000318.2"
## [1] "found 12 genes."
## [1] 21
## [1] "NID1" "ST6GALNAC5" "F3" "C2CD6"
## [5] "MEGF11" "OTOGL" "MACROD2" "CYP7B1"
## [9] "C12orf42" "TAFA1" "HES5" "ADD3-AS1"
## [13] "LCNL1" "AP000233.4" "MIR181A1HG" "LINC01036"
## [17] "RP1-45C12.1" "OBI1-AS1" "RNF217-AS1" "LINC02652"
## [21] "SOX2-OT" "LINC00504" "LINC01950" "RP11-582J16.4"
## [25] "LINC02389" "LINC02328" "RP11-103J8.1" "RP11-436D23.1"
## [29] "RP11-57G22.3" "RP11-437L7.2" "RP11-1289C17.1" "RP11-399K19.1"
## [33] "CTD-2297M2.1" "TENM2" "SLC5A11" "LINGO1"
## [37] "PDE3A" "GPR137C" "ZNF804B" "PLK5"
## [41] "KBTBD12" "DLEU2" "AC002127.4" "KCNMB2-AS1"
## [45] "LINC01252"
## [1] "found 20 genes."
## [1] 22
## [1] "SEZ6L" "CAP2" "TACC2"
## [4] "ARHGAP18" "PLEKHG4B" "MON1A"
## [7] "SLC43A2" "RAB39A" "C9orf153"
## [10] "KIF5C-AS1" "RP11-390F4.6" "LINC00877"
## [13] "TRMT9B" "CTD-2126E3.6" "MAP3K9"
## [16] "PDK3" "RASGRP2" "ADGRL1"
## [19] "ARHGAP15" "EBF4" "TICAM1"
## [22] "ZBTB46" "KIAA0513" "NKD1"
## [25] "CCDC40" "MVB12A" "CLVS2"
## [28] "RIT2" "ST3GAL2" "C1orf87"
## [31] "FAAH2" "PIK3CD" "VAT1L"
## [34] "SYT12" "PPP1R42" "LINC00862"
## [37] "LYRM4" "STARD10" "MTRNR2L1"
## [40] "RPPH1_ENSG00000259001" "RP11-35G9.5" "CASTOR2"
## [43] "RP11-465L10.14"
## [1] "found 35 genes."
## [1] 23
## [1] "LINC01630" "MTRNR2L8"
## [3] "LINC01374" "USH2A"
## [5] "SLC26A3" "STEAP1B"
## [7] "KLF2" "LGR6"
## [9] "RHBDL3" "ESYT3"
## [11] "SYTL3" "PTCHD1"
## [13] "GREM1" "SEMA3E"
## [15] "MRGPRF" "AC023469.1"
## [17] "AC003090.1" "AC064875.2"
## [19] "RP11-563D10.1" "LINC01320"
## [21] "RP11-154D17.1" "AC013463.2"
## [23] "RP11-305L7.3" "AC002066.1"
## [25] "RP11-384F7.1" "RP11-17A1.3"
## [27] "LINC02742" "RP11-79E3.2"
## [29] "LINC02208" "LINC01609"
## [31] "RP11-958J22.1" "RP11-20D14.3"
## [33] "RP11-507B12.2" "RP11-507B12.1"
## [35] "LINC00558" "MTRNR2L12"
## [37] "RMRP_ENSG00000269900" "SCARNA2_ENSG00000270066"
## [39] "RP11-154H23.4" "CH507-513H4.1"
## [41] "CH507-528H12.1" "RP11-596C23.6"
## [43] "RP11-379B18.8" "RP4-799O8.1"
## [45] "AC003099.2" "RP11-398J12.1"
## [1] "found 14 genes."
## [1] 24
## [1] "ANOS1" "MAMLD1" "KIAA1549L" "PDE8B"
## [5] "TFAP2E" "KCTD1" "SLC44A3" "LIX1"
## [9] "DUSP15" "PCED1B" "PRELID2" "SLC4A5"
## [13] "MAML3" "SULT1A2" "MAMDC2-AS1" "CTA-292E10.6"
## [17] "RP1-167A14.2" "RP1-223B1.1" "LINC01725" "RP1-230L10.1"
## [21] "LINC00407" "LEFTY1" "OSMR-AS1" "RP11-1252I4.2"
## [25] "RP4-785G19.5" "LINC00958" "DISC1FP1" "RP11-574F11.4"
## [29] "DGKB" "LRGUK" "DEPTOR" "ADCY1"
## [33] "FRMD3" "TOGARAM2" "AP001347.6" "XXbac-BPG55C20.7"
## [37] "RP11-69I8.3" "CYP1B1-AS1" "LINC00884" "AL163953.3"
## [41] "MIR4300HG" "LINC01094" "CTD-2054N24.2" "RP11-210M15.2"
## [45] "RP11-114N19.3"
## [1] "found 21 genes."
## [1] 25
## [1] "OSBPL3" "SYTL4" "UBE3D" "BICC1" "GFRA1"
## [6] "SPOCK1" "C4orf19" "MMP16" "RNF150" "LRRN2"
## [11] "MTSS1" "C1QTNF4" "ZNF497" "RNLS" "ROR1"
## [16] "SHISA6" "L3MBTL3" "SAMD13" "LINC01266" "AC097721.2"
## [21] "NPIPB2" "RP11-11N9.4" "CTXND1" "COL23A1" "SYNE2"
## [26] "TBC1D1" "RARB" "PPARGC1A" "ARSB" "CHD5"
## [31] "PRR12" "FCHO1" "THRB" "FAM107A" "SLC25A20"
## [36] "SPACA6" "PAX8-AS1" "RP5-921G16.1" "RP11-26J3.1" "RP11-298I3.1"
## [41] "CASC17" "AGBL1" "LINC02246"
## [1] "found 34 genes."
## [1] 26
## [1] "MYO16" "PPEF1" "EPB41L4B" "SGK2" "NT5DC3"
## [6] "FRK" "MASP1" "TESPA1" "GPNMB" "PLK2"
## [11] "ARHGAP27" "CCDC141" "C4orf45" "SSR4" "BAALC-AS2"
## [16] "CCDC124" "DCN" "CDH3" "ATP2B3" "CASS4"
## [21] "SLC7A5" "ADAP1" "EPHB6" "SUSD1" "DUSP1"
## [26] "PMEPA1" "EDA2R" "SLC6A6" "HAVCR2" "MICAL1"
## [31] "ARHGAP29" "EGF" "SLC43A1" "ITPR1" "CNKSR3"
## [36] "FBXO32" "CATIP" "ITGA2" "NT5DC2" "MOB3A"
## [41] "MB21D2" "HAUS7" "RP11-60A24.3"
## [1] "found 41 genes."
## [1] 27
## [1] "KCNN2" "IQCH" "LAMA4" "DPYSL3" "ENOX1" "ABCC4"
## [7] "FADS2" "ARRDC4" "ST6GAL2" "ABI3BP" "NDUFAF2" "TSPAN5"
## [13] "GPR156" "CA8" "GINS3" "IMMP2L" "MGAM" "SLC7A2"
## [19] "HSD17B14" "RNF24" "KAT8" "PPP1R13L" "B4GALT2" "DPP6"
## [25] "NCAN" "CCNH" "BCAS3" "COL6A2" "CNNM2" "DPYSL5"
## [31] "PDPN" "ABCA1" "FAT3" "ENOX2" "ZNF608" "PFKFB3"
## [37] "SLC35E3" "RGMA" "ABAT" "EFCAB2" "C19orf38" "EML6"
## [1] "found 42 genes."
## [1] 28
## [1] "NTN1" "IL7" "GABRA4" "RPS15"
## [5] "HSD11B1" "RPL36" "RPLP1" "PDE5A"
## [9] "RNF165" "FAU" "ZNF48" "SEPTIN1"
## [13] "PLD5" "KCNB2" "SP140L" "MT1X"
## [17] "EYS" "KCNMB2" "RPS18" "LUCAT1"
## [21] "RP11-348J24.1" "KCNG1" "ZFY" "RHOBTB1"
## [25] "ANGPT2" "PCDH11Y" "KCNN1" "TSPAN11"
## [29] "TNNT2" "NRP2" "HS3ST2" "AIF1L"
## [33] "C1QL1" "KCNH5" "PXDNL" "SPATA2L"
## [37] "FGF17" "ST8SIA3" "POTEG" "RP11-147G16.1"
## [41] "ETV5"
## [1] "found 38 genes."
## [1] 29
## [1] "TENM1" "TMSB10" "EFEMP1" "BEX1" "CACNA1A" "SHANK2"
## [7] "VWCE" "DLGAP2" "CNTN1" "RIMBP2" "CTNNA2" "SYT1"
## [13] "RBFOX1" "TGFB2" "PCSK5" "GLIS3" "CPE" "CLNK"
## [19] "MACF1" "PALLD" "SOX5" "ARHGEF4" "PCSK6" "ECE2"
## [25] "NCAM2" "SHANK1" "OXR1" "RBFOX3" "SLC20A2" "FRMPD4"
## [31] "DLGAP1" "FRMD5" "CNTNAP2" "SH3PXD2B" "CSMD1" "OPCML"
## [37] "CNTN2" "DUSP8" "ZFP36L1" "KCNIP4" "ARID5A" "SRGAP1"
## [43] "ZNF358" "NEAT1"
## [1] "found 43 genes."
## [1] 30
## [1] "WSCD2" "SLC8A3" "PLCB4" "CHODL"
## [5] "BNC2" "CYP4F12" "CYP4F3" "INSYN2B"
## [9] "LINC02814" "AC092684.1" "SOCS2-AS1" "LINC02326"
## [13] "RP11-116N8.1" "RP11-104E19.1" "MAPT-AS1" "RP11-793A3.2"
## [17] "RP11-354K4.2" "LINC00836" "LINC00842" "RP11-492O8.3"
## [21] "RP11-259G3.1" "RP11-154D6.3" "RP11-609L3.3" "RP1-20N4.2"
## [25] "ARHGAP6" "CCDC175" "ANGPT1" "SAMD3"
## [29] "METTL7B" "SAMD11" "LAMA2" "PLPP4"
## [33] "RP11-174G6.1" "RP11-90C4.1" "LINC01088" "RP11-346L1.2"
## [37] "LINC00609" "LINC02251" "RP11-259K15.2" "RP11-627D16.1"
## [41] "RP11-499F3.2" "RP11-114N1.1" "RP11-542F9.2" "RP5-1015P16.1"
## [45] "RP11-6L16.1"
## [1] "found 16 genes."
## [1] 31
## [1] "REEP1" "RASD1" "ADCY7" "TRIM5" "LPAR4" "FABP5"
## [7] "SVEP1" "SCG5" "AQP1" "KLHL13" "FOSL2" "GADD45B"
## [13] "NFATC2" "IGSF21" "ID3" "ITIH5" "RTN2" "JUND"
## [19] "RTN1" "CREB5" "ADAM12" "SEC24D" "KCNE4" "RASSF3"
## [25] "GDPD5" "ARHGAP35" "ATF3" "TMEM200A" "NFIL3" "FOS"
## [31] "JUNB" "CXXC5" "SPSB1" "PLEKHG5" "RND1" "PAWR"
## [37] "YOD1" "RGS6" "FAM110C" "MAFF" "TRDN" "CRYBB2"
## [1] "found 42 genes."
## [1] 32
## [1] "NRXN3" "PSD" "BCAS1" "RPH3A"
## [5] "SLC16A6" "CALY" "KIRREL3" "NDST3"
## [9] "JAM3" "GRIK1" "GALNTL6" "GRM7"
## [13] "CARNMT1-AS1" "RP11-170M17.1" "AC011288.2" "RP1-232L24.3"
## [17] "LINC02217" "C5orf17" "RP4-809F18.1" "LINC02254"
## [21] "PWRN1" "PRAG1" "RP11-239A17.1" "CTC-428H11.2"
## [25] "RP11-125D12.3" "RP11-320L2.1" "BAIAP3" "P2RX7"
## [29] "SEC14L5" "ATRNL1" "SCN2A" "SLC4A10"
## [33] "ST18" "CNTN5" "NLGN1" "SLC8A1"
## [37] "PDE2A" "CCK" "SHTN1" "CACNA1E"
## [41] "MMP17" "MEG3" "RP1-30E17.2" "RP11-190P13.2"
## [45] "IQCJ-SCHIP1"
## [1] "found 29 genes."
## [1] 33
## [1] "ARHGAP28" "PHACTR2" "ELL2" "FHAD1" "RNF175"
## [6] "HS3ST3A1" "RETREG1" "GFRA2" "STK32A" "SNX31"
## [11] "RP11-364L4.3" "APP-DT" "RP5-965G21.3" "ST6GALNAC2" "ST6GAL1"
## [16] "P3H2" "CLIP2" "JHY" "MAN1C1" "LRAT"
## [21] "TTC9" "SCN1A" "PARP8" "NFASC" "ARHGEF3"
## [26] "CFAP47" "SLITRK5" "TPST1" "COL24A1" "RCAN2"
## [31] "PRIMA1" "CAVIN1" "PLCXD3" "CHST6" "OVCH1"
## [36] "LINC00632" "CFI" "RP1-111D6.3" "SATB1-AS1" "CTD-2643I7.5"
## [41] "LINC01411" "LINC02506" "RP1-79C4.4" "RP11-403A3.3" "RP11-403A3.2"
## [1] "found 33 genes."
## [1] 34
## [1] "LRRC7" "SNCAIP" "SP140" "STS"
## [5] "ANKRD7" "B3GAT2" "PLAGL1" "GTDC1"
## [9] "UNC79" "ARSG" "SUMF1" "BEND6"
## [13] "SYCP2L" "GRIK2" "ALDH1A1" "PRTG"
## [17] "ANO5" "NEGR1" "RGS7" "PNMA3"
## [21] "KIAA0825" "LINC02649" "LINC00571" "AC072062.3"
## [25] "SNHG31" "RP11-154D6.1" "PKN2-AS1" "RP11-446H18.5"
## [29] "CXXC4-AS1" "SEMA6A-AS1" "RP11-673E1.1" "RP11-586K2.1"
## [33] "AB015752.3" "RP11-624D11.2" "RP11-798K3.2" "CRTC3-AS1"
## [37] "LINC00907" "ARRDC3-AS1" "RP4-681L3.3" "RP11-592G13.2"
## [41] "RP11-335E8.3" "RNF19A" "ZMAT3" "RP3-466I7.2"
## [1] "found 23 genes."
## [1] 35
## [1] "MAP2K6" "PDE10A" "GBE1" "PSG8" "HS3ST3B1"
## [6] "EPSTI1" "ANKRD33B" "FSTL5" "SGCD" "SLIT1"
## [11] "TENM3" "SOX1-OT" "AC007193.6" "HGF" "COL5A3"
## [16] "WFDC1" "XYLT1" "NAMPT" "UNC5B" "SPP1"
## [21] "CCND2" "LOXL1" "PTPRJ" "FREM2" "KCNJ16"
## [26] "PTMS" "ADORA1" "RANBP3L" "MAP1A" "LRRC8C"
## [31] "CSDC2" "HPSE2" "ARPP21" "FZD8" "NME9"
## [36] "PCP4" "ZNF98" "DNM3" "AC003991.3" "SPRY4-AS1"
## [41] "LINC01619" "CEACAM16-AS1" "PKD1L3"
## [1] "found 37 genes."
## [1] 36
## [1] "FAR2" "FAM117B" "HMGA2" "UNC5D"
## [5] "TMEM130" "ZCCHC18" "EPHX4" "STOX2"
## [9] "RNF212" "WNT7B" "RANBP17" "LINC01829"
## [13] "LINC00499" "RP11-745L13.2" "RP11-20I20.2" "RP11-313M3.2"
## [17] "RP11-175O15.1" "NIPAL3" "ABCA7" "CDH20"
## [21] "TUSC3" "ARHGEF18" "LGI1" "CHRNE"
## [25] "SEM1" "ZSWIM6" "RAP1GAP2" "ADGRB3"
## [29] "SLC44A5" "ABCB9" "JAZF1" "IQCK"
## [33] "CADM2" "FIGN" "SLC25A18" "LHFPL6"
## [37] "MAML2" "OSBP2" "FLRT2" "NKAIN2"
## [41] "KIF9-AS1" "PTCHD1-AS" "OLMALINC" "TMEM161B-AS1"
## [1] "found 34 genes."
## [1] 37
## [1] "UPP2" "PAPPA2" "RGS22" "SLC9B1"
## [5] "C11orf65" "SUGCT" "ZBTB44-DT" "CASC2"
## [9] "LEKR1" "COL5A2" "AC007277.3" "RP11-344B5.2"
## [13] "TARID" "ZRANB2-AS2" "LINC00271" "RFX3-AS1"
## [17] "AF131217.1" "UFL1-AS1" "RP11-195C7.1" "LINC01376"
## [21] "LINC01358" "CDKN2B-AS1" "RP11-550I24.2" "H2AZ1-DT"
## [25] "LINC02355" "RP11-268P4.5" "LINC01340" "LINC02615"
## [29] "LIX1-AS1" "C8orf37-AS1" "LINC02740" "LINC02745"
## [33] "RP11-266O8.1" "LINC02320" "RP11-111A21.1" "RP11-16B13.1"
## [37] "RP11-739G5.1" "PSMD7-DT" "RP11-157E16.1" "RP11-964E11.3"
## [41] "RP11-341N18.1" "RP11-788A4.3" "RP5-892C22.1" "RP11-215I16.3"
## [45] "RP11-446J8.1"
## [1] "found 8 genes."
## [1] 38
## [1] "ANKRD24" "MROH8" "SPATA6L" "TEX9"
## [5] "ADAP2" "MALRD1" "APTR" "AP001628.6"
## [9] "LMCD1-AS1" "CTC-329D1.2" "IDH2-DT" "SYNPO2L-AS1"
## [13] "RP11-382N13.7" "TMEM38A" "RFX2" "DAAM1"
## [17] "RFX4" "IQCA1" "PATJ" "LRMDA"
## [21] "TBX6" "FAM151B" "ADCY8" "NRG2"
## [25] "NAV2" "FAM174B" "CCDC30" "NOL4L"
## [29] "TMEM229B" "AC004951.6" "RP5-864K19.4" "RP11-348F1.3"
## [33] "WARS2-AS1" "LINC00342" "LINC01137" "LINC01135"
## [37] "DPH6-DT" "RP11-148E17.1" "RP3-414A15.10" "RP1-158P9.2"
## [41] "TAPT1-AS1" "ATP6V0D1-DT" "RP11-514P8.10" "RP11-799O21.2"
## [45] "RP11-125C10.1"
## [1] "found 22 genes."
## [1] 39
## [1] "CHI3L1" "FHDC1" "WARS1" "BTG2"
## [5] "HES4" "IER5L" "LINC01503" "MSC-AS1"
## [9] "RP11-380P13.1" "BCL6-AS1" "RP11-640F22.1" "MCUB"
## [13] "SYT7" "KLF6" "TESC" "KLHL4"
## [17] "HELB" "COL5A1" "UNC13C" "CBLN2"
## [21] "CDH18" "SLC24A2" "CFAP161" "COX7A1"
## [25] "PGM2L1" "DEPP1" "HTR1E" "SLC38A11"
## [29] "SLC26A5" "KCNH7" "TNFRSF25" "RP11-513I15.6"
## [33] "MIR34AHG" "RP1-187B23.1" "KRTAP5-AS1" "IQCM"
## [37] "AC067956.1" "SHISA9" "CTC-340A15.2" "LINC01322"
## [41] "PTCHD4" "LINC02223" "RP11-624C23.1" "MIR23AHG"
## [45] "RP11-4D11.1"
## [1] "found 29 genes."
## [1] 40
## [1] "RRAGD" "FAM107B" "SRPX" "CLIC5"
## [5] "CRISPLD1" "TRIM22" "PLXNC1" "CA3"
## [9] "CIITA" "PROS1" "F5" "CCDC26"
## [13] "RP11-157I4.4" "RP11-124B13.1" "RP1-41C23.1" "RP11-255O19.2"
## [17] "AC006296.4" "VCAN" "KITLG" "FRY"
## [21] "RASL12" "CCL2" "SOHLH2" "ACVR1C"
## [25] "BEST3" "GFPT2" "HNMT" "LMNTD1"
## [29] "FBN1" "NPNT" "CLIC4" "SLCO3A1"
## [33] "NHS" "DPYD" "OSTN" "SLC6A9"
## [37] "HRAT92" "LINC02869" "RP5-1198O20.4" "RP11-469A15.2"
## [41] "RP11-146I2.1" "MAFG-DT" "RP3-365E2.1" "RP11-103P4.1"
## [1] "found 30 genes."
Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4158769 222.2 7959177 425.1 NA 7959177 425.1
## Vcells 8940574 68.3 29538339 225.4 65536 29518146 225.3## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5